The main warning I would have is to avoid any part that may have algal growth (i.e. shells) and any part of the digestive system. This will help you avoid contamination. We had some problems with contamination when working with amplifying mtDNA in some very small aquatic snails. At first we just digested to whole specimen and got some bad contamination from different algal species. After this we removed the snail from the shell and this worked will.
Since you are working with marine bivalves you may also want to avoid gonadal tissue do to doubly uniparental inheritance (DUI). DUI is common in many marine bivalves and can make examining your sequences a little difficult. Here is a good paper on this topic.